Conflicts:

	Makefile

diff --git a/Makefile b/Makefile
index 6a432a1..7bc53b9 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -10,8 +10,8 @@ help::
        @echo ">> Help"
        @echo ">>>> Download"
        @echo "---- To register new/Modified source codes. ----"
-       @echo " $$ make git-add         or git-add[-all|-data|-tutorial|-optional|-others]" 
-       @echo " $$ make git-commit      or git-commit[-all|-data|-tutorial|-optional|-others]" 
+       @echo " $$ make git-add         or git-add[-all|-data|-tutorial|-optional|-others|-others2]" 
+       @echo " $$ make git-commit      or git-commit[-all|-data|-tutorial|-optional|-others|-others2]" 
        @echo " $$ git tag " 
        @echo " $$ git tag newtag "
        @echo " $$ make git-push        or git-push[-all|-data|-tutorial|-optional|-others]" 
@@ -30,6 +30,7 @@ help::
        @echo "     [-tutorial] : tutorial"
        @echo "     [-optional] : optional(for documents)"
        @echo "     [-others] : other source codes for utils"
+       @echo "     [-others2] : other source codes for utils"
        @echo "     [-all] : all"
        @echo ""
        @echo ">>>> Setting"
@@ -82,6 +83,9 @@ git-add-tutorial::
 git-add-others::
        cd others; git add . 
 
+git-add-others2::
+       cd others2; git add . 
+
 git-commit-all:: git-commit git-commit-data git-commit-optional git-commit-tutorial git-commit-others
 
 git-commit::
@@ -99,6 +103,9 @@ git-commit-tutorial::
 git-commit-others::
        cd others; git commit 
 
+git-commit-others2::
+       cd others2; git commit 
+
 git-backup::
        git push $(EOS_GIT_BACKUPSITE) master  --tags
 
@@ -213,3 +220,9 @@ git-clone-others: git-init-others
        then \
                git clone --depth 1 $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_OTHERS) ./ ; \
        fi
+       cd others ; git remote add others $${EOS_GIT_USER}@$(EOS_GIT_REPOSITRY_OTHERS)
+
+git-init-others2::
+       if [ ! -d others2 ] ; then mkdir others2; fi
+       cd others2 ; git remote add others2 $${EOS_GIT_USER}@$(EOS_GIT_REPOSITRY_OTHERS)
+

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAddValue b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAddValue
index 8ca9c37..69f8c05 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAddValue and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAddValue differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis
index f4d7bfd..4d5546f 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation
index 197894c..1dbefd5 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageInfo
index 4141521..00fbc64 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageInfo and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageInfo differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization
index 03182d7..364b4b4 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo
index f7e6dc1..b47d749 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/pdbChargeFit b/hostdepend/X86LINUX64/bin/X86LINUX64/pdbChargeFit
index 85ad983..9cc3eaf 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/pdbChargeFit and b/hostdepend/X86LINUX64/bin/X86LINUX64/pdbChargeFit differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.a b/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.a
index 8a6b14b..5306e27 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.a and b/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.a differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.so b/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.so
index c236f1b..c4f4cef 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.so and b/hostdepend/X86LINUX64/lib/X86LINUX64/libCluster.so differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a b/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a
index c6c4ef3..76ccac9 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a and b/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.so b/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.so
index 82a5317..e5e93b4 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.so and b/hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.so differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.a b/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.a
index b7b4a76..19552c7 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.a and b/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.a differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.so b/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.so
index aef5612..f3d5aa6 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.so and b/hostdepend/X86LINUX64/lib/X86LINUX64/libeosCuda.so differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a b/hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a
index 7f7f2a9..32d2e98 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a and b/hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/clusterLogRead.sharedo b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/clusterLogRead.sharedo
index 9db58c9..6f0d32a 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/clusterLogRead.sharedo and b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/clusterLogRead.sharedo differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/eosCuda.sharedo b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/eosCuda.sharedo
index bccbf78..b1224d8 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/eosCuda.sharedo and b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/eosCuda.sharedo differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageClusterAnalysis.sharedo b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageClusterAnalysis.sharedo
index 3c1f89c..b43316b 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageClusterAnalysis.sharedo and b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageClusterAnalysis.sharedo differ

diff --git a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageFFT.sharedo b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageFFT.sharedo
index 66d9ed1..cfbe0ee 100644 (file)
Binary files a/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageFFT.sharedo and b/hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageFFT.sharedo differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a
index 7f7f2a9..32d2e98 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a
index 9045513..862e38a 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.so b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.so
deleted file mode 100755 (executable)
index 581bfb5..0000000
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.so and /dev/null differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageClusterAnalysis.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageClusterAnalysis.sharedo
index 3c1f89c..b43316b 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageClusterAnalysis.sharedo and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageClusterAnalysis.sharedo differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo
index 66d9ed1..cfbe0ee 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/st9mESV2 b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/st9mESV2
new file mode 100644 (file)
index 0000000..84ff998
Binary files /dev/null and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/st9mESV2 differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/.Depend
index 5396ec8..bd02b0b 100644 (file)
--- a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/.Depend
@@ -7,26 +7,27 @@ clusterLogAnalysis.o: clusterLogAnalysis.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/Memory.h /usr/include/stdlib.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /home/people/tacyas/Eos/include/Vector.h \
@@ -35,20 +36,21 @@ clusterLogInit.o: clusterLogInit.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Memory.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h /usr/include/stdlib.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h ../inc/Cluster.h
@@ -56,22 +58,21 @@ clusterLogRead.o: clusterLogRead.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /home/people/tacyas/Eos/include/Memory.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
- /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
- /home/people/tacyas/Eos/include/Memory.h /usr/include/stdlib.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/posix2_lim.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /home/people/tacyas/Eos/include/String.h \
@@ -80,6 +81,8 @@ clusterLogRead.o: clusterLogRead.c /usr/include/stdio.h \
  /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
@@ -95,21 +98,22 @@ clusterLogUtil.o: clusterLogUtil.c \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/Memory.h /usr/include/stdio.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -118,16 +122,17 @@ clusterLogWrite.o: clusterLogWrite.c /usr/include/stdlib.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
- /usr/include/sys/types.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/math.h /usr/include/bits/huge_val.h \
  /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
@@ -135,12 +140,12 @@ clusterLogWrite.o: clusterLogWrite.c /usr/include/stdlib.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/string.h /usr/include/xlocale.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/Memory.h \
  /home/people/tacyas/Eos/include/mrcImage.h \

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/Makefile b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/Makefile
index 28e9069..a429553 100755 (executable)
--- a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/Makefile
+++ b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/Makefile
@@ -22,6 +22,8 @@ $(SHAREDLIB): $(SHAREDOBJ)
        @COMPILEDOBJ=`ls $(SHAREDOBJ)` ; echo "#### Compiled Objects"; echo $${COMPILEDOBJ};  echo "################"; \
        $(SHARED) $(SHAREDLIB) $${COMPILEDOBJ} 
 
+debug: $(LIBNAMEDEBUG) $(LIBNAMECUDAGDB)
+
 $(LIBNAMEDEBUG): $(OBJDEBUG)
        @echo LIBNAME:$(LIBNAMEDEBUG)
        $(AR) rs $(LIBNAMEDEBUG) $(OBJDEBUG)

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/clusterLogRead.sharedo b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/clusterLogRead.sharedo
index 9db58c9..6f0d32a 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/clusterLogRead.sharedo and b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/clusterLogRead.sharedo differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a
index 8a6b14b..5306e27 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a and b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.debug.a b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.debug.a
index 6c4cfa0..2466fb7 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.debug.a and b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.debug.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.so b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.so
index c236f1b..c4f4cef 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.so and b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.so differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo
index bccbf78..b1224d8 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo and b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a
index b7b4a76..19552c7 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a and b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so
index aef5612..f3d5aa6 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so and b/hostdepend/X86LINUX64/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
index 383befc..abe9a39 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
@@ -1,14 +1,15 @@
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -19,26 +20,27 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageAddValue.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -49,12 +51,12 @@ init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageAddValue.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
@@ -62,14 +64,15 @@ mrcImageAddValue.o: mrcImageAddValue.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -80,12 +83,12 @@ mrcImageAddValue.o: mrcImageAddValue.c /usr/include/stdio.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageAddValue.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
@@ -93,18 +96,20 @@ mrcImageAddValue.o: mrcImageAddValue.c /usr/include/stdio.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Array.h \
  /home/people/tacyas/Eos/include/lmrcImageAddValue.h \
- /home/people/tacyas/Eos/include/mrcImage.h
+ /home/people/tacyas/Eos/include/mrcImage.h \
+ /home/people/tacyas/Eos/include/eosCuda.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
@@ -112,14 +117,15 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
 util.o: util.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/mrcImageAddValue b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/mrcImageAddValue
index 8ca9c37..69f8c05 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/mrcImageAddValue and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/mrcImageAddValue differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/.Depend
index ebaefa5..7a445d4 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/.Depend
@@ -1,14 +1,15 @@
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -19,26 +20,27 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageClusterAnalysis.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -49,12 +51,12 @@ init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageClusterAnalysis.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
@@ -62,14 +64,15 @@ mrcImageClusterAnalysis.o: mrcImageClusterAnalysis.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -78,12 +81,12 @@ mrcImageClusterAnalysis.o: mrcImageClusterAnalysis.c /usr/include/stdio.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h ../inc/config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h ../inc/config.h \
  ../inc/../inc/mrcImageClusterAnalysis.h \
  /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
@@ -107,14 +110,15 @@ mrcImageClusterAnalysis.o: mrcImageClusterAnalysis.c /usr/include/stdio.h \
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
@@ -122,14 +126,15 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
 util.o: util.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis
index f4d7bfd..4d5546f 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/.Depend
index 9393267..a51af6c 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/.Depend
@@ -1,14 +1,15 @@
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -19,26 +20,27 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageDilation.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -49,12 +51,12 @@ init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageDilation.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
@@ -62,14 +64,15 @@ mrcImageDilation.o: mrcImageDilation.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -80,12 +83,12 @@ mrcImageDilation.o: mrcImageDilation.c /usr/include/stdio.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageDilation.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
@@ -97,14 +100,15 @@ mrcImageDilation.o: mrcImageDilation.c /usr/include/stdio.h \
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
@@ -112,14 +116,15 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
 util.o: util.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation
index 197894c..1dbefd5 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageInfo/src/X86LINUX64/mrcImageInfo b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageInfo/src/X86LINUX64/mrcImageInfo
index 4141521..00fbc64 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageInfo/src/X86LINUX64/mrcImageInfo and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageInfo/src/X86LINUX64/mrcImageInfo differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcInfo/src/X86LINUX64/mrcInfo b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcInfo/src/X86LINUX64/mrcInfo
index f7e6dc1..b47d749 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcInfo/src/X86LINUX64/mrcInfo and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcInfo/src/X86LINUX64/mrcInfo differ

diff --git a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbChargeFit/src/X86LINUX64/pdbChargeFit b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbChargeFit/src/X86LINUX64/pdbChargeFit
index 85ad983..9cc3eaf 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbChargeFit/src/X86LINUX64/pdbChargeFit and b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbChargeFit/src/X86LINUX64/pdbChargeFit differ

diff --git a/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/.Depend
index 7668eed..9d8eedd 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/.Depend
@@ -1,14 +1,15 @@
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -19,26 +20,27 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -49,12 +51,12 @@ init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
@@ -63,21 +65,15 @@ mrcImageOrientationSearchBySimultaneousMinimization.o: \
  /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
- /usr/include/limits.h /usr/include/bits/posix1_lim.h \
- /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
- /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -87,7 +83,13 @@ mrcImageOrientationSearchBySimultaneousMinimization.o: \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h ../inc/config.h \
  ../inc/../inc/mrcImageOrientationSearchBySimultaneousMinimization.h \
- /home/people/tacyas/Eos/include/genUtil.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/Memory.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h \
@@ -105,14 +107,15 @@ mrcImageOrientationSearchBySimultaneousMinimization.o: \
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
@@ -120,14 +123,15 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
 util.o: util.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization b/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization
index 03182d7..364b4b4 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization and b/hostdepend/X86LINUX64/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/X86LINUX64/mrcImageOrientationSearchBySimultaneousMinimization differ

diff --git a/hostdepend/X86LINUX64ICC/src/Objects/DataManip/mrcImage/src/X86LINUX64ICC/libmrcImage.so b/hostdepend/X86LINUX64ICC/src/Objects/DataManip/mrcImage/src/X86LINUX64ICC/libmrcImage.so
deleted file mode 100755 (executable)
index 9dc585e..0000000
Binary files a/hostdepend/X86LINUX64ICC/src/Objects/DataManip/mrcImage/src/X86LINUX64ICC/libmrcImage.so and /dev/null differ

diff --git a/hostdepend/X86LINUX64ICC/src/Objects/General/eosCuda/src/X86LINUX64ICC/eosCuda.c b/hostdepend/X86LINUX64ICC/src/Objects/General/eosCuda/src/X86LINUX64ICC/eosCuda.c
deleted file mode 120000 (symlink)
index 6ea5bb3..0000000
--- a/hostdepend/X86LINUX64ICC/src/Objects/General/eosCuda/src/X86LINUX64ICC/eosCuda.c
+++ /dev/null
@@ -1 +0,0 @@
-../eosCuda.c
\ No newline at end of file

diff --git a/src/Config/Template/ToolsTemplate.Dir/src/Makefile b/src/Config/Template/ToolsTemplate.Dir/src/Makefile
index 56aa068..7beb110 100755 (executable)
--- a/src/Config/Template/ToolsTemplate.Dir/src/Makefile
+++ b/src/Config/Template/ToolsTemplate.Dir/src/Makefile
@@ -210,17 +210,20 @@ install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
 
 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) 
        @echo ---- Installing to bin
+       @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
        then \
                mkdir $(DSTDIR)/$(OSTYPE); \
        fi
-       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) ]; \
+       @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
        then \
+               echo "Compilation is complete"; \
                $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+               $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+       else \
+               echo "Compilation is incomplete. $(OBJECTNAME)"; \
        fi
-       @$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE)
-       @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
-       @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @echo ---- end of bin
 
 install-wish:

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageClusterAnalysis.c b/src/Objects/DataManip/mrcImage/src/lmrcImageClusterAnalysis.c
index 98a16ed..1e7ca43 100755 (executable)
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageClusterAnalysis.c
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageClusterAnalysis.c
@@ -47,6 +47,9 @@ lmrcImageClusterAnalysisDistanceToLog(FILE* fpt, int n, int m, int prevM, int pr
 double
 lmrcImageDistanceCalc0(mrcImage* out, mrcImage* cor, mrcImage* clusterN, mrcImage* clusterM, int numN, int numM, lmrcImageClusterAnalysisInfo* linfo) {
        double distance = 0;
+       mrcImageParaTypeRealCoord offset;
+
+       offset.x = offset.y = offset.z = 0;
 
        DEBUGPRINT("n lmrcImageDistanceCalc0:");
        switch(linfo->mode) {
@@ -78,7 +81,10 @@ lmrcImageDistanceCalc0(mrcImage* out, mrcImage* cor, mrcImage* clusterN, mrcImag
                                                           clusterN, clusterM, 
                                       numN, numM, 
                                       linfo->mode);
-                       *out = *clusterN;
+                       //*out = *clusterN;
+                       out->Header = clusterN->Header;
+                       mrcInit(out, NULL);
+                       lmrcImageCopy(out, clusterN, offset);
                        cor->Image = NULL;
                  }
                  break;

diff --git a/src/Objects/DataManip/transform/src/lmrc2Dto3D.h b/src/Objects/DataManip/transform/src/lmrc2Dto3D.h
index 3d80a0e..7dab365 100755 (executable)
--- a/src/Objects/DataManip/transform/src/lmrc2Dto3D.h
+++ b/src/Objects/DataManip/transform/src/lmrc2Dto3D.h
@@ -30,7 +30,8 @@
 
 typedef enum lmrc2Dto3DMode {
        mrc2Dto3DModeSimpleBackProjection = 0,
-       mrc2Dto3DModeFilteredBackProjection = 1
+       mrc2Dto3DModeFilteredBackProjection = 1,
+       mrc2Dto3DModeWeightedBackProjection = 2
 } lmrc2Dto3DMode;
 
 typedef struct lmrc2Dto3DInfo {

diff --git a/src/Objects/General/Cluster/src/clusterLogRead.c b/src/Objects/General/Cluster/src/clusterLogRead.c
index 23b7ab4..aefc2a4 100755 (executable)
--- a/src/Objects/General/Cluster/src/clusterLogRead.c
+++ b/src/Objects/General/Cluster/src/clusterLogRead.c
@@ -10,8 +10,9 @@
 */
 /* $Log$ */
 #include <stdio.h>
+/*
 #include <values.h>
-
+*/
 #include "Memory.h"
 #include "String.h"
 #include "../inc/Cluster.h"

diff --git a/src/Objects/Makefile.org b/src/Objects/Makefile.org
deleted file mode 100644 (file)
index ad84110..0000000
--- a/src/Objects/Makefile.org
+++ /dev/null
@@ -1,5 +0,0 @@
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc

diff --git a/src/Tools/Makefile.orig b/src/Tools/Makefile.orig
deleted file mode 100755 (executable)
index ad84110..0000000
--- a/src/Tools/Makefile.orig
+++ /dev/null
@@ -1,5 +0,0 @@
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageAddValue/src/Makefile b/src/Tools/mrcImage/mrcImageAddValue/src/Makefile
index 56aa068..7beb110 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAddValue/src/Makefile
+++ b/src/Tools/mrcImage/mrcImageAddValue/src/Makefile
@@ -210,17 +210,20 @@ install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
 
 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) 
        @echo ---- Installing to bin
+       @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
        then \
                mkdir $(DSTDIR)/$(OSTYPE); \
        fi
-       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) ]; \
+       @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
        then \
+               echo "Compilation is complete"; \
                $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+               $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+       else \
+               echo "Compilation is incomplete. $(OBJECTNAME)"; \
        fi
-       @$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE)
-       @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
-       @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @echo ---- end of bin
 
 install-wish:

diff --git a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.c b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.c
index 7df26dc..4be8ad2 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.c
+++ b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.c
@@ -15,7 +15,6 @@ static char __sccs_id[] = "%Z%mrcImageClusterAnalysis ver%I%; Date:%D% %Z%";
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>                  
-#include <values.h>                  
 #define GLOBAL_DECLARATION
 #include "../inc/config.h"
 

diff --git a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
index 062c929..00f921a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
+++ b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
@@ -1 +1,39 @@
-/bin/bash: mrcImageClusterAnalysis: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageClusterAnalysis</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageClusterAnalysis</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageClusterAnalysis
+Options:
+    [-I[nput array of file]In                  (NULL      )] :Essential :InputDataFiles
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-O[utput]           ] :Optional  :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
+    [-N[umberOfClusters] N                   (1         )] :Optional  :Number of clusters
+    [-Min[imumCorrelation]Min                 (0.0       )] :Optional  :Minimum: Correlation: Conditions for ending
+    [-Iter[ation]        ] :Optional  :IterationFlag
+    [-A[uto]R[otation]   AutoRotation        (72        )] :Optional  :AutoRotation: rotation divided by this value
+    [-A[utoRot]Range     ARMin               (0         )ARMax               (360       )] :Optional  :AutoRotationRange
+    [-A[uto]R[otation]iter[ation]AutoRotationIteration(2         )] :Optional  :AutoRotationIteration
+    [-A[uto]R[otation]MethodAutoRotationMethod  (0         )] :Optional  :Method for Correlation for Auto Rotation
+    [-M[odeForCorrelation]correlationMode     (19        )] :Optional  :Correlation Mode for AutoRotation
+    [-pvm                ] :Optional  :Parallel Analysis by PVM
+    [-pvmList            pvmList             (NULL      )] :Optional  :pvmList: Input
+    [-Log                Log                 (stdout    )] :Optional  :Log: Output
+    [-Log2               Log2                (NULL      )] :Optional  :Log2: Output: ClusterNode Only
+    [-LogIn              LogIn               (NULL      )] :Optional  :previousLog: Input
+    [-prevF[ileNum]      prevFileNum         (0         )] :Optional  :previousLogFileNum: Input
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         )] :Optional  :Mode
+----- Additional Usage -----
+Distance between clusters: mode
+       mode 0: By Correlation
+       mode 1: By Euclid Distance
+       mode 2: By Ward Method (default) : Euclid Length (no rotation) or its square (rotation)
+       mode 3: By Ward Method using Linear Correlation : (1 - Correlation)/(1 + Correlation)
+       mode 4: By Linear Correlation :                   (1 - Correlation)/(1 + Correlation)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDilation/src/Makefile b/src/Tools/mrcImage/mrcImageDilation/src/Makefile
index 56aa068..a99b8c4 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDilation/src/Makefile
+++ b/src/Tools/mrcImage/mrcImageDilation/src/Makefile
@@ -214,11 +214,12 @@ $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME
        then \
                mkdir $(DSTDIR)/$(OSTYPE); \
        fi
-       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) ]; \
+       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) -a -x $(OSTYPE)/$(OBJECTNAME) ]; \
        then \
+               echo "TEST"; \
                $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
        fi
-       @$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE)
        @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @echo ---- end of bin

diff --git a/src/Tools/mrcImage/mrcImageInfo/src/Makefile b/src/Tools/mrcImage/mrcImageInfo/src/Makefile
index 56aa068..d85f344 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageInfo/src/Makefile
+++ b/src/Tools/mrcImage/mrcImageInfo/src/Makefile
@@ -214,12 +214,15 @@ $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME
        then \
                mkdir $(DSTDIR)/$(OSTYPE); \
        fi
-       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) ]; \
+       @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
        then \
+               echo "Installing"; \
                $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+       else \
+               echo "Compilation is incomplete."; \
        fi
-       @$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE)
-       @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+       @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); 
        @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
        @echo ---- end of bin
 

diff --git a/src/Tools/mrcImage/mrcInfo/src/Makefile b/src/Tools/mrcImage/mrcInfo/src/Makefile
index 56aa068..cc1f32f 100755 (executable)
--- a/src/Tools/mrcImage/mrcInfo/src/Makefile
+++ b/src/Tools/mrcImage/mrcInfo/src/Makefile
@@ -214,14 +214,14 @@ $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME
        then \
                mkdir $(DSTDIR)/$(OSTYPE); \
        fi
-       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) ]; \
+       @if [ -x $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) -a -x $(OSTYPE)/$(OBJECTNAME) ]; \
        then \
                $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+               $(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+               echo ---- end of bin ; \
        fi
-       @$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE)
-       @$(CHMOD) 555 $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
-       @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
-       @echo ---- end of bin
 
 install-wish:
        @if [ -d wish ]; \

diff --git a/src/Tools/pdbUtil/pdbChargeFit/Config/Define.inc b/src/Tools/pdbUtil/pdbChargeFit/Config/Define.inc
index 7d0ddbe..f96420f 100755 (executable)
--- a/src/Tools/pdbUtil/pdbChargeFit/Config/Define.inc
+++ b/src/Tools/pdbUtil/pdbChargeFit/Config/Define.inc
@@ -1,4 +1,4 @@
 OBJECTNAME = pdbChargeFit
-EXTRA_LIB  =
+EXTRA_LIB  = $(LIBCUDA)
 EXTRA_CCOPTS =
 EXTRA_INC =

diff --git a/src/Tools/pdbUtil/pdbChargeFit/src/pdbChargeFit.c b/src/Tools/pdbUtil/pdbChargeFit/src/pdbChargeFit.c
index e8eaf63..20151eb 100755 (executable)
--- a/src/Tools/pdbUtil/pdbChargeFit/src/pdbChargeFit.c
+++ b/src/Tools/pdbUtil/pdbChargeFit/src/pdbChargeFit.c
@@ -62,11 +62,11 @@ void lpdbChargeFit(pdbChargeFitInfo *info)
 
 
        tmpPdb.nAtom=0;
-       tmpPdb.PDB=NULL;
+       tmpPdb.top = tmpPdb.PDB=NULL;
        inFixCA.nAtom=0;
-       inFixCA.PDB=NULL;
+       inFixCA.top = inFixCA.PDB=NULL;
        inMoveCA.nAtom=0;
-       inMoveCA.PDB=NULL;
+       inMoveCA.top = inMoveCA.PDB=NULL;
        
        lengthV=floatVectorInit(lengthV,3);
 

diff --git a/src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c b/src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c
index 7d5f765..1f1c961 100755 (executable)
--- a/src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c
+++ b/src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c
@@ -110,6 +110,7 @@ additionalUsage()
        fprintf(stderr, "-m Option\n");
        fprintf(stderr, "    %d:SimpleBackProjection\n", mrc2Dto3DModeSimpleBackProjection);
        fprintf(stderr, "    %d:FilteredBackProjection\n", mrc2Dto3DModeFilteredBackProjection);
+       fprintf(stderr, "    %d:WeightedBackProjection\n", mrc2Dto3DModeWeightedBackProjection);
        fprintf(stderr, "-single 0|1 \n");
        fprintf(stderr, "    0: tilt axis is parallel to x-axis\n");
        fprintf(stderr, "    1: tilt axis is parallel to y-axis\n");

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.c b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.c
index 7919e65..0243947 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.c
+++ b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.c
@@ -9,7 +9,6 @@
 #
 */
 #include <stdio.h>
-#include <values.h>
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>                  

diff --git a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.html b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.html
index 8b3fd50..c69489b 100755 (executable)
--- a/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.html
+++ b/src/Tools/rec3d/mrcImageOrientationSearchBySimultaneousMinimization/src/mrcImageOrientationSearchBySimultaneousMinimization.html
@@ -1 +1,80 @@
-/bin/bash: mrcImageOrientationSearchBySimultaneousMinimization: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageOrientationSearchBySimultaneousMinimization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageOrientationSearchBySimultaneousMinimization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageOrientationSearchBySimultaneousMinimization
+Options:
+    [-I[nputFileList]    In                  (NULL      )] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-dt[heta]           dtheta              (1         )] :Optional  :dtheta
+    [-dp[si]             dpsi                (1         )] :Optional  :dpsi
+    [-m[odeof]s[election]ms                  (0         )] :Optional  :modeofselection
+    [-i[nitial]r[andom]d[ata]ird                 (1         )] :Optional  :InitialRandomData
+    [-M[ax]C[ount]       MC                  (100       )] :Optional  :MaxCount
+    [-F[ileName]H[eader] FileNameHeader      (EulerAngle)] :Optional  :FileNameHeader
+    [-m[odeof]i[nitial]d[ada]mid                 (0         )] :Optional  :modeofinitialdata
+    [-i[nputFile]i[nitial]d[ata]InInitial           (NULL      )] :Optional  :InputDataFileOfInitialData
+    [-m[odeof]s[tart]p[oint]msp                 (0         )] :Optional  :mode of start point
+    [-m[odeof]a[ngular]a[rea]maa                 (0         )] :Optional  :mode of angular area
+    [-p[revious]dt[heta] pdtheta             (0         )] :Optional  :previous dtheta
+    [-p[revious]dp[si]   pdpsi               (0         )] :Optional  :previous dpsi
+    [-m[ode]L[calculation]modeL               (0         )] :Optional  :Mode of L calculation
+    [-m[ode]T[hreshold]A[ngularweight]modeTA              (0         )] :Optional  :Mode of Threshold of AngularWeight
+    [-m[ode]c[alculation]a[rea]modeCA              (0         )] :Optional  :mode of Lvalue of calculation area
+    [-t[hreshold]c[alculation]a[rea]TCA                 (0         )] :Optional  :Threshold of Lvalue of calculation area
+    [-m[ode]f[ix]        modeF               (0         )] :Optional  :mode of fix
+
+----- ModeSelection -----
+-ms : 0 : random
+    : 1 : myself (-ird)
+
+----- Mode --------------
+-m : 0 : input data --> sinogram
+   : 1 :            --> sinogramFT
+
+----- Angle -------------
+-dt    : DEGREE
+-dp    : DEGREE
+-pdt   : DEGREE
+-pdp   : DEGREE
+
+----- ModeOfInitialData -------------
+-mid : 0 : There is not initial data
+       1 : There is     initial data (-iid)
+
+----- ModeOfLcalculation -------------
+-mL : 0 : differential of length
+      1 : differential of phase
+      2 : addition to derivation1D (multiply)
+      3 : addition to derivation1D (difference)
+
+----- ModeOfThresholdAngularWeight -------------
+-mTA : 0 : 1.0e-4
+       1 : 1 degree
+       2 : dpsi
+
+----- ModeOfStartPoint -------------
+-msp : 0 : origin
+       1 : initial data (-iid)
+
+----- ModeOfAngularArea -------------
+-maa : 0 : all area
+       1 : aroud previous delta (-pdt -pdp)
+
+----- ModeOfCalculationArea -------------
+-mca : 0 : all area
+       1 : cut under -tca(1/angstrom)
+
+----- ModeOfFix -------------
+-mf : 0 : don't fix one plane
+      1 :       fix one plane (first file is fixed)
+
+</PRE>
+</BODY>
+</HTML>